Depends on what you think have. Post some pictures of the coins in question and maybe we can help out.
The mystery error. Here's the thing - we can't read minds. What's clear to YOU is what YOU'RE looking at. Less so for us. Here's the bad news - if it's that subtle, it's probably nothing.
The fact that it impinges into other design elements? Have you checked to see if they're ALL like that? That's always Step #1.
Die Chip.. Nothing Major I keep them only because they look cool.. I don't care if they carry a premium or not.
I'd recommend a 2x2 file box and high quality flips. If you use Saflips (I recommend them highly.), try NOT to move the box much. The flips are chemically fine, but stiff and can on occasion scratch coins with too much jostling.